Variant report

Variant	rs6710763
Chromosome Location	chr2:64068788-64068789
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:517)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:517 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:64067662-64069172	HUVEC	blood vessel:	n/a	n/a
2	SIN3A	chr2:64067241-64069212	GM12878	blood:	n/a	n/a
3	POLR2A	chr2:64067418-64069792	K562	blood:	n/a	n/a
4	POLR2A	chr2:64067196-64069274	HL-60	blood:	n/a	n/a
5	EP300	chr2:64068487-64069202	GM12878	blood:	n/a	chr2:64068777-64068793
6	MAX	chr2:64067261-64069107	H1-hESC	embryonic stem cell:	n/a	n/a
7	SP4	chr2:64067437-64069169	H1-hESC	embryonic stem cell:	n/a	chr2:64068388-64068404 chr2:64067994-64068010
8	POLR2A	chr2:64067693-64069196	HepG2	liver:	n/a	n/a
9	CTCF	chr2:64068680-64068830	HAc	cerebellar:	n/a	n/a
10	POLR2A	chr2:64066467-64077414	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr2:64067196-64069886	ProgFib	skin:	n/a	n/a
12	CTCF	chr2:64068720-64068870	GM06990	blood:	n/a	n/a
13	KAP1	chr2:64067660-64070291	U2OS	brain:	n/a	n/a
14	ZNF143	chr2:64067536-64069084	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr2:64068612-64069232	SK-N-MC	brain:	n/a	n/a
16	TAF1	chr2:64067470-64069236	H1-hESC	embryonic stem cell:	n/a	n/a
17	HNF4A	chr2:64068663-64068967	HepG2	liver:	n/a	chr2:64068877-64068899
18	POLR2A	chr2:64067707-64069234	HUVEC	blood vessel:	n/a	n/a
19	TBP	chr2:64068577-64069213	GM12878	blood:	n/a	n/a
20	POLR2A	chr2:64067017-64069463	HUVEC	blood vessel:	n/a	n/a
21	GTF2B	chr2:64068629-64069059	K562	blood:	n/a	n/a
22	STAT5A	chr2:64067482-64069174	GM12878	blood:	n/a	chr2:64068607-64068619 chr2:64067694-64067706
23	POLR2A	chr2:64067515-64069485	PFSK-1	brain:	n/a	n/a
24	REST	chr2:64068614-64069219	PFSK-1	brain:	n/a	chr2:64068680-64068690
25	CTCF	chr2:64068720-64068870	GM12865	blood:	n/a	n/a
26	CTCF	chr2:64068660-64068810	AG09309	skin:	n/a	n/a
27	MAX	chr2:64067483-64070170	Hela-S3	cervix:	n/a	n/a
28	IRF1	chr2:64068583-64069638	K562	blood:	n/a	n/a
29	HDAC2	chr2:64068743-64068982	K562	blood:	n/a	n/a
30	POLR2A	chr2:64067326-64069633	K562	blood:	n/a	n/a
31	MYBL2	chr2:64067599-64070273	HepG2	liver:	n/a	n/a
32	TAF1	chr2:64067643-64069065	HepG2	liver:	n/a	n/a
33	CTCF	chr2:64068680-64068830	BJ	skin:	n/a	n/a
34	CHD1	chr2:64067067-64074747	H1-hESC	embryonic stem cell:	n/a	chr2:64068850-64068860 chr2:64068822-64068832 chr2:64068878-64068888 chr2:64067996-64068006
35	POLR2A	chr2:64067434-64069928	Hela-S3	cervix:	n/a	n/a
36	MYC	chr2:64068645-64068802	HUVEC	blood vessel:	n/a	n/a
37	POLR2A	chr2:64067224-64069354	HUVEC	blood vessel:	n/a	n/a
38	E2F6	chr2:64068508-64068961	K562	blood:	n/a	chr2:64068668-64068680 chr2:64068875-64068884
39	POLR2A	chr2:64067549-64069258	SK-N-SH	brain:	n/a	n/a
40	MAX	chr2:64067522-64069978	ECC-1	luminal epithelium:	n/a	n/a
41	POLR2A	chr2:64067485-64069228	GM12891	blood:	n/a	n/a
42	CTCF	chr2:64068539-64069051	GM12878	blood:	n/a	chr2:64068913-64068931
43	CTCF	chr2:64068640-64068790	HPAF	blood vessel:	n/a	n/a
44	RAD21	chr2:64068570-64069019	SK-N-SH_RA	brain:	n/a	n/a
45	POLR2A	chr2:64067445-64069126	GM12878	blood:	n/a	n/a
46	HCFC1	chr2:64067197-64069270	Hela-S3	cervix:	n/a	n/a
47	TEAD4	chr2:64067791-64069001	H1-hESC	embryonic stem cell:	n/a	n/a
48	ELF1	chr2:64067431-64069249	MCF-7	breast:	n/a	n/a
49	REST	chr2:64067437-64069483	H1-neurons	neurons:	n/a	chr2:64068680-64068690
50	BRCA1	chr2:64068483-64068807	GM12878	blood:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:63816373..63818974-chr2:64066021..64069792,3	MCF-7	breast:
2	chr2:64068314..64068983-chr4:100009769..100010303,2	NB4	blood:
3	chr2:64052299..64060510-chr2:64066102..64071144,11	MCF-7	breast:
4	chr2:64066407..64070482-chr2:64071096..64075382,10	MCF-7	breast:
5	chr15:64388019..64388832-chr2:64068186..64068837,2	Hela-S3	cervix:
6	chr2:64052304..64056068-chr2:64066396..64069697,6	K562	blood:
7	chr2:64066782..64070718-chr2:64080924..64091365,11	MCF-7	breast:
8	chr15:42783198..42783888-chr2:64068476..64069063,2	Hela-S3	cervix:
9	chr2:64065422..64070588-chr2:64080925..64083417,5	K562	blood:
10	chr11:67397170..67397676-chr2:64068288..64068862,2	Hela-S3	cervix:
11	chr2:64066677..64069203-chr2:64081708..64084913,3	MCF-7	breast:
12	chr2:64053563..64056956-chr2:64065611..64068830,7	K562	blood:
13	chr19:50180136..50180856-chr2:64068295..64068838,2	Hela-S3	cervix:
14	chr1:19577823..19578483-chr2:64068731..64069281,2	Hela-S3	cervix:
15	chr2:64068765..64069430-chr5:138677613..138678199,2	Hela-S3	cervix:
16	chr19:49468534..49469455-chr2:64068708..64069486,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
UGP2	TF binding region
ENSG00000053372	Chromatin interaction
ENSG00000014641	Chromatin interaction
ENSG00000120727	Chromatin interaction
ENSG00000092531	Chromatin interaction
ENSG00000126457	Chromatin interaction
ENSG00000197894	Chromatin interaction
ENSG00000127463	Chromatin interaction
ENSG00000103994	Chromatin interaction
ENSG00000246090	Chromatin interaction
ENSG00000028528	Chromatin interaction
ENSG00000087086	Chromatin interaction
ENSG00000143951	Chromatin interaction
ENSG00000169764	Chromatin interaction
ENSG00000167799	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10183479	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11691987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12713498	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs13018690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1440002	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17619753	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs193031	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2969395	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs34777730	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs4233930	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs4538187	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4671073	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs6546029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6546030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6546032	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6546035	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs6715992	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6732746	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6755646	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7590399	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013375	chr2:63969820-64231550	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6710763	ETFDH	trans	cerebellum	SCAN
rs6710763	UGP2	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64065800-64071000	Active TSS	Liver	Liver
2	chr2:64066800-64069800	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr2:64066800-64070600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:64067000-64070000	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr2:64067000-64073200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr2:64067000-64075800	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr2:64067000-64076400	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr2:64067200-64069800	Active TSS	Brain Anterior Caudate	brain
9	chr2:64067200-64069800	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr2:64067200-64070000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:64067200-64070000	Active TSS	Fetal Kidney	kidney
12	chr2:64067200-64070000	Active TSS	Pancreas	Pancrea
13	chr2:64067200-64070000	Active TSS	Rectal Smooth Muscle	rectum
14	chr2:64067200-64070200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:64067200-64070200	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr2:64067200-64070200	Active TSS	Gastric	stomach
17	chr2:64067200-64070400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:64067200-64070800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:64067200-64071600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:64067200-64071800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:64067200-64072000	Active TSS	Aorta	Aorta
22	chr2:64067200-64072000	Active TSS	Fetal Muscle Trunk	muscle
23	chr2:64067200-64072200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr2:64067200-64072200	Active TSS	Colonic Mucosa	Colon
25	chr2:64067200-64072400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:64067200-64073200	Active TSS	Left Ventricle	heart
27	chr2:64067200-64073400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr2:64067400-64068800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
29	chr2:64067400-64069800	Active TSS	H1 Cell Line	embryonic stem cell
30	chr2:64067400-64070000	Active TSS	GM12878-XiMat	blood
31	chr2:64067400-64070200	Active TSS	Esophagus	oesophagus
32	chr2:64067400-64070200	Active TSS	Lung	lung
33	chr2:64067400-64070200	Active TSS	Sigmoid Colon	Sigmoid Colon
34	chr2:64067400-64070400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr2:64067400-64070400	Active TSS	Ovary	ovary
36	chr2:64067400-64071000	Active TSS	Thymus	Thymus
37	chr2:64067400-64071400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:64067400-64072200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr2:64067400-64074000	Active TSS	H9 Cell Line	embryonic stem cell
40	chr2:64067600-64069000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:64067600-64069000	Active TSS	Spleen	Spleen
42	chr2:64067600-64069200	Active TSS	Primary T cells from cord blood	blood
43	chr2:64067600-64069200	Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr2:64067600-64069200	Active TSS	Fetal Heart	heart
45	chr2:64067600-64069400	Active TSS	Primary B cells from peripheral blood	blood
46	chr2:64067600-64069400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr2:64067600-64069400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr2:64067600-64069400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
49	chr2:64067600-64069400	Active TSS	Duodenum Mucosa	Duodenum
50	chr2:64067600-64069400	Active TSS	Fetal Stomach	stomach

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